Blender knife tool options
N-gons with a hole

Currently holed-ngons (e.g. a doughnut section) are not supported. If in the cutting process you are creating one of those, the software will try its best in finding a way to continue anyway (in this case by splitting the ngon in two and as a side effect deleting th inner face).

In the picture below you can see the difference of behaviour of the command upon the same mesh but with different topology:



I suggest to continue knife projecting the shape as you were doing and then simply re-fill the boundary with a new face. Just select the hole boundary and press F or with another method (e.g. fill holes operator).